Protein Alignment Reports

Protein alignment reports show the details of the alignment for a protein against the predicted translated gene. To see an alignment report for a protein, click the grey bar representing its alignment on the protein page.

QUERY The internal query number and length of the query for the run that retrieved all the hits shown on the Protein Page.
Hit The name of the database the hit comes from, the database's ID and description of the protein, and in brackets, the organism name.
SCORE The alignment score for the protein against the translated gene.
EVALUE The expectation value for the alignment (the number of times a match against the database is expected to occur by chance alone).
Alignment Length The length of the aligning region, including gaps in the protein and in the translated gene.
IDENTITIES The percentage of the alignment length that contains identical amino acids in both the translated gene and the protein.
SIMILARITIES The percentage of the alignment length that contains amino acids that are similar in the translated gene and the protein.
GAPS The total number of gaps in the protein sequence for which the translated gene has sequence.
QUERY START and QUERY END Coordinates of the first and last amino acids in the alignment, relative to the start of the translated gene.
HIT START and HIT END Coordinates of the first and last amino acids in the alignment, relative to the start of the protein.
- The coordinates of the first and last amino acid on each line, relative to the start of the translated gene and the start of the protein, are shown along the left and right margins.
- Vertical bars indicate identities.
- Dots indicate similarities.
- Dashes indicate gaps in the alignment.